Donnie Berkholz › Likes

"One problem that I am facing is convincing colleagues of the utility of an Open Access publication. ... Not everyone operates on large grants. Many lab budgets leave very little room to buy a new laptop, let alone pay for an OA publication (typically the price of two of said laptops)." - Mickey Kosloff from Bookmarklet

Good points here. Proving a rival to current closed-access or setting a precedent to get grant-givers to make line-items for OA publication are good in an abstract/aggregate level, but the individual lab decision-maker is thinking on a lot more concrete terms. Perhaps, some sort of Impact Factor or "open access journal news" to add credence/credibility can substitute? - Benjamin Tseng

I'm glad you've made the point -- I talk about it with students who will have to make these kinds of decisions in the coming years -- and it's a tough one: ideological belief against practical action. Maybe we need a kind of OA investment account where interest can be accrued over the life of a grant. Okay, not realistic...government subsidies, maybe;-)? - Mickey Schafer

Also check out his other post: http://blog.zacharyvoase.com/post... Awesome awesome stuff. Also, I'm more than a little relieved to find out I'm not crazy. Or at least that I have company in crazy town depending on the interpretation. - Paul J. Davis

Nice post, but I don't think it would sell me on using RDF. It's not like you can't agree on syntax and meaning (or even use ontologies) without RDF. Better to show how RDF helps deal with the fact that not all databases are ever going to agree on a single set of non-overlapping concepts for describing their data, and -- more important -- with more fundamental disagreements (such as what an organism even is). - Eric Jain

"like" as in "wtf?" - Bill Hooker

Perhaps that's their undercover advocacy for Open Access to the methods sections? - Daniel Mietchen

Yes! Finally!!! - Alejandro Montenegro

"The acid test: if I see electrons pushed around, it's chemistry" http://scienceblogs.com/terrasi... - Iddo Friedberg

I really want to "like" that comment, but I guess I'll settle with the whole post... - Donnie Berkholz

Imo journals should simply refuse to publish without full M&M details, sufficient for replication. - Bill Hooker

Update: My "Carters" reacted friendly to my friendly inquiry, and we provided each other with more details on the experiments, but it is still next to impossible to reconcile our results, and neither they nor me currently have funds for this line of research - another case where baseline grants would be handy. - Daniel Mietchen

"The Internet has changed scientific publishing in many ways, some good and some bad. No one would deny that it is easier to find papers on a particular subject than ever before. Looking up papers in Index Medicus or by browsing Current Contents has long been replaced by online searches on Medline or even Google Scholar. This has not necessarily improved our understanding of the literature, but it certainly provides a quick way to feel up to date." - Abhishek Tiwari from Bookmarklet

I agree that the ability to track readership and download stats for my papers would be *extremely* valuable. It will probably just become more so as online papers approach the next-gen prototypes so you could even tell which sections and figures are viewed most. - Donnie Berkholz

press release: http://www.sciencenews.org/view... - Michael Kuhn

@Michael: I guess you've seen the list on Wikipedia: http://en.wikipedia.org/wiki... - Michael Kuhn

It's nice to see other journals following the system Biology Direct has. - Alejandro Montenegro

Transparency has to be good... - Peter Murray

"The majority of papers published" - why not all? - AJCann

This is really good! - Björn Brembs

excellent b/c addresses delivery and environment as well as design -- most instructional sites don't do this, though Michael Alley on posters (http://www.writing.engr.psu.edu/posters...) and especially power point presentations (http://www.writing.engr.psu.edu/slides...) are generally excellent, student-friendly guides -- not necessarily humorous, unless you like squirrels. - Mickey Schafer

"What if scientists, instead of rushing to publish or perish, chose to cooperate? Sean Cutler decided to do “a little experiment,” as he calls it, and you can see the results in the forthcoming issue of Science. " - Abhishek Tiwari from Bookmarklet

By determining goals, method of achievement, and providing feedback competition can be designed to encourage cooperation. - Mike Chelen

Obviously sorting isn't the most parallizable test, but sorting on a dual-core machine took nearly twice as long with bashreduce. I probably should test some quad or 8-core machines before passing judgement. - Chris Miller

"What you're doing is very clever, and I see how it's useful, but how is it science?" - Abhishek Tiwari

"It's not. How is your research science?" - Abhishek Tiwari

They don't make it very easy to send a copy online. - Donnie Berkholz

Bother your US friends? - Bora Zivkovic

"The usual N.I.H. research grant is from $250,000 and $300,000 and runs for four years, and each grant supports six or seven full-time or part-time jobs, Dr. Kington said. To provide a quicker economic impact, the institutes may also award two-year grants of $500,000 per year, but soliciting proposals and judging them could take up to a year." - Andrew Su

There is more good news for UC journal authors. The California Digital Library (CDL) and Springer have signed a ground-breaking agreement in which UC-authored articles accepted for publication in most of the 1700 Springer journals will be published using Springer "Open Choice" which brings with it full and immediate access to all readers. This means that UC authors will pay no additional publication fees in order for their articles to be immediately and fully open to all. Under the agreement, articles will be published under a license in which authors retain the right to distribute and re-use their articles freely. - Jason Stajich

To invoke the "Open Choice" option, UC authors will select a UC campus affiliation from a drop-down box that appears on the acceptance screen which authors must complete once an article has been accepted for publication. A message on the acceptance screen will indicate that the Open Choice option is being made available to them at no charge. (The Open Choice publication fee would... more... - Jason Stajich

http://www.universityofcalifornia.edu/news... - Jason Stajich

Do any of you use SciTopics? - Steve Koch

"Now, most scientists are familiar with the “cataloging system” of scientific journals, they’ve been reading them their entire careers. Everyone has their own filters, their own rankings of which journals are more interesting, or publish better work than others. And all kinds of tools are available for filtering things down to just the relevant essentials for keeping up with your own field. But even so, most people that I talk to are left with more useful, relevant articles that they need to read than they have time to get to. These are not articles that should be filtered out. These are important, quality findings of direct relevance to their own work. And there are too many of them without even factoring in a need to keep up with science in general and see what developments in other fields can be applied to one’s own." - Alexey from Bookmarklet

"A company's lawsuit against researchers should not be allowed to intimidate others." Note: free to access online (registration may be required). - Maxine from Bookmarklet

pullquote: "I will review 10 manuscripts per year free of charge. For anything over that number, I will request $50 per review. This will apply to all the publishers of scientific journals. If more scientists join in this action, the publishers will soon realize that they are here because of the scientists and not the other way around." - Bill Hooker

Looks like some of our comments above crossed, Bill. I certainly don't share your view of what you call "Glam Mags" though. - Maxine

Alleged that the source of the outbreak was 2 research labs - Neil Saunders from Bookmarklet

"There's a lesson here: don't throw anything away." - Shannon McWeeney

This is why it's better to dry SDS-PAGE gels and keep them too, rather than just scan them (something I have to admit, I don't always do). You can always cut out the bands and run mass spec years down the track .... - Andrew Perry

*sigh* - Deepak Singh from Bookmarklet

Michael, very true. The part that got me was the quote and I find it difficult to get over the apparent statement that doing "scientific research and development in a residential area" was a violation of zoning laws. - Deepak Singh

about, "a special flavor of Linux that can be automatically optimized and customized for just about any application or need. Extreme performance, configurability and a top-notch user and developer community." - Czar from Bookmarklet

Some great discussion in the comments for this one on Nature site. But will any of the excellent points raised actually be addressed by NIH? How likely they will be able to limit institutional overhead or number of grants per PI. - Jason Stajich

Including "test" - Roland Krause

I agree it is an imperfect system but reform in the NIH is a huge elephant in the room. The salary cap idea is a good one and so are grant caps. But what reform would get a new investigator the same attention and access to a funded grant as an established investigator? That specific concern needs to be addressed constructively in order to build more parity into the system and translate novel ideas into everyday science. - Aarthy

I'm posting 2-3 snippets from this insightful article: [...Why write a comment when you could be doing something more “useful”, like writing a paper or a grant? Furthermore, if you publicly criticize someone’s paper, there’s a chance that that person may be an anonymous referee in a position to scuttle your next paper or grant application....] - Ntino

[...Some scientists will object that contributing to Wikipedia isn’t really science. And, of course, it’s not if you take a narrow view of what science is, if you’ve bought into the current game, and take it for granted that science is only about publishing in specialized scientific journals. But if you take a broader view, if you believe science is about discovering how the world... more... - Ntino

Like Einstein, we have a small group of trusted collaborators with whom we exchange questions and ideas when we are stuck. Unfortunately, most of the time even our collaborators aren’t that much help. They may point us in the right direction, but rarely do they have exactly the expertise we need. Is it possible to scale up this conversational model, and build an online collaboration... more... - j1m

I have a feeling some of you will have something to say - Deepak Singh from Bookmarklet

great letter, thanks! "whole profession looks deeply unattractive to anybody with a grain of sense" - true - Alexey

The actual link is http://www.harpers.org/archive... (sorry for the broken link above). - Michael Nielsen

Yes, sorry about that. I posted the correct link on the OP. This is just a factoid from Harper's Index, but it's from a direct NIH report. - Todd Harris from twhirl